Objectives: This meta-analysis aimed to evaluate congenital malformations in infants conceived by assisted reproductive techniques (ART), compared with infants conceived spontaneously. Methods: In this study, available resources searched to find relevant articles included PubMed, ScienceDirect, Scopus, Google Scholar, Cochrane, ProQuest, Iranmedex, Magiran, and Scientific Information Database. After extracting the necessary information from evaluated articles, meta-analysis on the articles' data was performed using Stata version 11.2. Results: In this study, from a total of 339 articles, extracted from the initial investigation, ultimately 30 articles were selected for meta-analysis that assessed the use of ART on the risk of congenital abnormalities and some birth complications on 5 470 181 infants (315 402 cases and 5 154 779 controls). The odds ratio (95% confidence interval [CI]) for low birth weight was 1.89 (95% CI, 1.36 to 2.62), preterm labor 1.79 (95% CI, 1.21 to 2.63), cardiac abnormalities 1.43 (95% CI, 1.27 to 1.62), central nervous system abnormalities 1.36 (95% CI, 1.10 to 1.70), urogenital system abnormalities 1.58 (95% CI, 1.28 to 1.94), musculoskeletal disorders 1.35 (95% CI, 1.12 to 1.64), and chromosomal abnormalities in infants conceived by ART was 1.14 (95% CI, 0.90 to 1.44), which were all statistically significant, except chromosomal abnormalities. Conclusions: The risk of congenital abnormalities and some birth complications were significantly higher in ART than normal conception, while chromosomal abnormalities were not; therefore, the application of ART should be selected individually for patients by detailed assessment to reduce such risks in the population.