This cross-sectional study investigates specialization preference of medical students in Cairo, Ain Shams and El-Azhar Medical Schools using a stratified systematic random sample of 428 students and house officers (199 females and 229 males). They represent 5% of all second, fifth year students and house officers from all three universities. In addition 31 female students of El-Azhar were followed up to the final year and house officer year. The aim of the study is to compare students specialization preference with PHC needs. The questionnaire used comprised besides demographic data like age, sex, origin, maternal and paternal education and occupation also factors influencing the specialization preference like motive for choosing medical education, lecturer's personality, subject content, future location and setting intention. The distribution of specialization preference was found significantly different with educational year, sex, maternal education and occupation, father's occupation, socioeconomic standard, reason for choosing medical study and content attraction of the subject. Major subjects like surgery, medicine and gynaecology and obstetric were preferred significantly more by males, students with non-medical fathers, of lower SES, those who choose medicine for prestige and help of people, and who were attracted by the content of subject, while vis versa for pediatric and other specializations like cardiology, ophthalmology, clinical pathology and psychiatry among others. The follow-up study indicated that female students of El-Azhar tended to gynaecology and obstetric (from 32.3% to 42.1%) orienting themselves toward community needs being themselves to 34.1% from rural areas. The multiple regression analysis indicated that the best subset of variables influencing specialization preference are SES, maternal education, study reason, father occupation, sex, future setting and location. Students preferences are far from the PHC needs.