Congenital malformations [CM) affect 2-3% of all births and are the leading causes of perinatal deaths and also infant mortality and morbidity. Both genetic and environmental factors can cause birth defects. This study aimed at accurate diagnosis to detect the frequency of different types of the CM and evaluating the risk factors [genetic and environmental] implicated in developing these anomalies. A case-control study was conducted on 522 cases during the period from June 2001 to June 2003. For comparison, 506 normal control group was randomly selected. The frequency of isolated cases was 31.03% [162/522 cases]. The highest frequency of CM involved the Urogenital systems [56.2%], followed in descending order by Central Nervous System [14.8%], Eye anomalies [13%], Congenital Heart Disease [9.3%], Cleft lip and/or palate [4.9%] and Gastro-intestinal anomalies [1.8%]. There was a significant association between neonatal risk factors as male sex [OR = 2.77; Cl: 1.85-4.19], low birth weight [OR = 4.53; CI: 2.60-7.92], and preterm [OR = 6.82; CI: 2.68-18.73] and the occurrence of CM. Other risk factors as twinning did not have a significant influence on the frequency of CM, while breech presentation had a significant protective effect from CM. There was a positive association between the maternal risk factors as young maternal age [< 25 years; OR = 1.53; Cl: 1.03-2.27], positive consanguinity [OR = 4.63; CI: 3.13-6.85], repeated abortion [OR = 6.59; CI: 2.83-16.19] and CM. Maternal exposure to drugs such as female sex hormones, antibiotics, and analgesics, as well as maternal illness during the 1st trimester of pregnancy, had a significant effect on the frequency of CM. Although, pre-eclamapsia, oligohydramnios, and polyhydramnios are known to be complicated with CM, this study could not verify this association. The study emphasizes that determination of etiology of CM is an important step towards primary prevention.