Mr Lowry is charged with fraud, forgery and criminal association in a trial set to last until December. He denies the charges.
"I've got to clear my name," he said outside court. "My business is built on trust and I've done nothing wrong. I can't be tainted with even a hint of fraud."
Last year the Portuguese financial regulators, eager to demonstrate that financial and telecommunications deregulation offered no sanctuary for shady operators, pounced on Mr Lowry's telephone share-selling business and clapped him in jail on suspicion of swindling hundreds of investors.
Mr Lowry says the Portuguese do not understand the nature of his operations, which followed widely-used US practices.
He claims that the authorities' overhasty intervention destroyed the market for his shares, which were perfectly sound. He avows that the case against him is based on nothing more than unsubstantiated suspicion.
Liverpool-born Mr Lowry, 54, a graduate of Queen's University Belfast, has a distinguished career in Britain and the US as a law academic, tax consultant and investment broker.
He was detained on 22 April 1997 when police raided the Lisbon office of Paramount Portugal, a subsidiary of a Swiss share-dealing company that Mr Lowry set up in 1995 for a client who subsequently fell ill and died.
The prosecutor alleges that Paramount Portugal, employing more than 50 expatriate staff, telephoned investors around the world and persuaded them to buy shares in tiny American companies that proved worthless or of little value.
The prosecution claims that hundreds of people were defrauded of millions of pounds.
Police swooped on Paramount after Portugal's financial markets regulator, the CMVM, received complaints leading it to suspect the operation might be a scam.
"Scores of people complained they had lost large sums of money investing in worthless share certificates," said a CMVM spokeswoman.
Mr Lowry says he investigated Denmark, Ireland and Spain before opting for Portugal as base for the spin-off from the Swiss operation "purely on financial grounds: it had by far the cheapest labour costs".
He took Portuguese legal advice and was assured that if he steered clear of Portuguese stock and Portuguese clients he would not have to register the company - a consideration that tipped the balance in favour of Portugal.
On 22 March this year the Swiss federal banking commission closed the parent company, Paramount Securities and Trust, for violating a Swiss law introduced on 1 February 1997 that tightened rules on security dealing.
"This company had no address, no board of directors, no auditing company, nothing it needed to be a supervised dealer, so we closed it down," says Dina Balleyguier, legal spokeswoman for the Swiss banking commission.
She added: "In addition, we received complaints from a worrying number of clients from 1996 indicating big trouble with this company.
"We suspected fraud because Paramount was selling shares of a New Zealand company it owned that had no market value and the company had no activities. Clients were told beautiful things about that company that were not exact, and that's fraud.
"If Paramount had been a fit and proper business we would have allowed it to adapt to the new regulations, but our liquidator didn't find any documents relating to the activity of the company. They did not respond to our letters and we had great fears for the interests of our investors."
Mr Lowry was detained for a year before being charged, and he was refused bail seven times before his trial opened last month. For 17 months he has shared a five-person cell with 13 others.
Lisbon's Caxias prison authorities were reluctant to admit journalists, so I pretended to be an old friend in order to meet Mr Lowry, embracing him warmly in the prison's cafeteria-like visiting area.
"It's difficult being locked up with 13 people 21 hours a day, 24 hours if it's raining," he says. "But now I'm charged I can read the file a year on and see what the police put in. It's a story built up in secret; there's no evidence.
"I think they realised in June last year they'd made a mistake and thought 'Cripes, they've got the wrong guy', but there's no way to go back or say sorry."
Mr Lowry's prolonged detention without charge, and perceived irregularities in the police investigation and legal procedure, prompted Edward Fitzgerald QC, a British human rights lawyer, to pursue a complaint against Portugal on Mr Lowry's behalf at the European Commission of Human Rights in Strasbourg.
"Portugal has signed the European Convention on Human Rights, but hasn't updated its penal code since the days of the dictator Antonio Salazar, when it was usual to detain suspects for a year without charge or evidence," said Gudrun Parasie, a barrister assisting Mr Lowry with his human rights suit. "Portugal's has one of the worst penal systems in Europe."
Craig Heesch, a retired Los Angeles policeman and former FBI undercover operative, is in Lisbon mobilising support for his friend Mr Lowry, with whom he used to collaborate in investigating white-collar crime in US off-shore trusts.
"I'm convinced he's innocent," says Mr Heesch, who has rented a flat in nearby Cascais with his wife to be on hand during the trial.
He said: "International telesales are perfectly legal in the US. Mr Lowry took Portuguese legal advice to comply with Portuguese regulations before setting up in Lisbon, and the companies whose shares he sold were genuine.
"Complaints date from after the raid on Paramount, which obviously ruined the market."
Mr Heesch rejects the claims of the Swiss Banking Commission, saying the body has no authority to investigate criminal fraud. "They've subjected Paramount Switzerland to an ordinary administrative closing that affects many companies in Switzerland that don't follow their laws," he says.
Mr Lowry supplies glowing references from Professor William Twyning, a British lawyer, and Don Rogers, a former FBI special agent who met Mr Lowry through Mr Heesch. Each has drawn up a detailed report claiming to establish Mr Lowry's bone fides and rebutting allegations against him.
Joao Silva Herdeiro, a lawyer, represents 16 of some 500 clients he says are eligible to claim compensation from Paramount.
"We have clients who went to the US to check if the companies they had bought shares in really existed, and they verified they were no more than mailboxes, legal entities without any material activities.
"If they had really existed, they would have survived the closure of Paramount, which was only the broker."
Jan Engelund, a Danish owner of a computer and telecommunications company, says he thought he was entrusting his money to a regulated Swiss broker when he invested in DW Filters, a start-up company producing a water filter for poor countries, and Global Connect Direct , which offered cheap international telephone connections by buying from big firms at a cut rate.
"I smelled a rat when I received no response to letters and faxes. I went to the DWF address in Florida but there was no sign of the company.
"The maintenance man at the building said he'd never heard of it. The GCD's address turned out to be a letter box in a small shop whose owner said he had never seen anyone open the box," he said.
Mr Engelund declined to say how much he invested in the two companies, but says he lost it all. Mr Lowry says Mr Engelund made only cursory inquiries and the companies were closed for Christmas holidays.