All charges stemming from two alleged sexual assaults currently pending against former Harvard-affiliated doctor Arif Hussain will be tried together, but the prosecution may not mention Hussain's previous rape conviction in the upcoming trial because that case is presently on appeal, a Middlesex County superior court judge ruled yesterday.

After Judge Andrew G. Meyer's decision. Hussain's lawyers challenged the legitimacy of some prosecution evidence in the second day of motions before Hussain's trial begins.

Hussain is accused of raping one woman and sexually assaulting another while they were patients under his care at Waltham Hospital in 1978 Hussain and two other doctors at a Harvard-affiliated hospital were convicted last June of raping a nurse the summer before.

Defense attorneys argued Monday that the two current cases should not be severed because the two attacks allegedly took place in, the same hospital and some of the same witnesses would be asked to testify about both incidents and might confuse the jury.

The two incidents were considered together in a probable cause hearing last November and Judge Andrew Meyer ruled yesterday the two alleged assaults are related and that they should be decided in the same trial.

Defense attornies charged yesterday that Assistant District Attorney William H. Kettlewell illegally used secret testimony from a grand jury hearing about the case last spring in his investigation.

Thomas C. Brot. the chief defense lawyer, called Kettlewell and district attorneys from the counties where the assaults took place to the witness stand to determine when Kettlewell obtained the disputed information.

Meyer denied Monday the defense's motions to bar press and public from the courtroom and a defense request to change the trial location because of alleged prejudicial publicity.

Hussain's trial is expected to begin after the judge rules on one more defense motion and jury selection is completed.