The findings indicated that amoxicillin, cephalosporins and nitrofurantoin were not associated with birth defects.
Although the absolute risks for birth defects were small, physicians should consider prescribing other antibiotics when treating patients with infections during pregnancy.
Senior author Anick Berard said that infections during pregnancy are frequent and should be treated.
Berard added that the study highlights safer options for treatment of infections, more specifically urinary tract infections or pulmonary infections, at least during the first trimester of pregnancy.
Researchers analysed information on 1,39,938 live births in Quebec, Canada, between 1998 and 2008.
Clindamycin, doxycycline, quinolones, macrolides and phenoxymethylpenicillin were linked to organ-specific malformations.
The research is published in journal of Clinical Pharmacology.