Despite three and a half hours of sometimes heated questioning by the prosecution, a composed Dr. Arif Hussain yesterday testified before a packed Middlesex County Courtroom that he is innocent of separate charges of rape and sexual assault lodged against him by two former female patients at Waltham Hospital.

The 31-year-old anesthesiologist, who worked at Harvard-affiliated Brigham and Women's Hospital until he was convicted last year of raping a nurse, was the final witness in his own defense in the highly publicized five-week trial. The 12-member jury, which has not been told of Hussain's previous conviction, is expected to begin deliberations tomorrow after final arguments are presented.

Hussain now faces charges of raping one woman in her Waltham Hospital bed on March 26, 1978 and attempting to rape a second woman in the same hospital on October 19 of the same year. Hussain served as an intern at the Waltham facility at the time.

The doctor acknowledged that he had given both women examinations late at night, despite a warning from superiors after the first incident not to conduct such examinations without a nurse present.

Hussain quietly replied "no" when Asst. Dist. Atty. William H. Kettlewell '73 asked him if he had taped the first woman and sexually assaulted the second one.

The first alleged victim, a 36-year-old mother of five, has said that Hussain injected her with morphine, tied her down and taped her. But witnesses have testified that the day of the alleged rape the woman did not complain of being raped and that she only said that Hussain had entered her room and inserted his finger into her vagina.

The doctor said yesterday that he had given the woman a rectal examination and that in her drugged state she had mistaken that for a sexual advance.

Both alleged victims in the case filed formal charges after Hussain had been accused along with two other doctors of raping a Brigham and Women's nurse.

Kettlewell also questioned the necessity and the propriety of Hussain's second late-night examination, which the doctor said he conducted because he was concerned about the woman's health and had been ordered to make the check by another doctor.

The prosecutor argued that Hussain should not have left his post in the Waltham Coronary Care Unit to perform tests that the nurses on the alleged victim's floor could have performed Kettlewell further noted the discrepancy between the estimated two minutes that the tests should have taken and the six to eight minutes that Hussain testified he had been in the room of the second victim.

Earlier in the trial, chief defense attorney Thomas C Troy said Hussain's testimony in the trial would "show the world what sort of human being he is."

But the defense yesterday questioned the doctor for less than 30 minutes and brought up no new issues.