Background: Assisted reproductive technology (ART) nowadays plays a major role in the treatment of infertility, with the most frequently used techniques being in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). The objective of this study is to analyze pregnancies achieved using these ART techniques and their correlations with the prematurity and congenital malformations rates. Methods: This is an observational retrospective longitudinal study that includes 814 newborns conceived through an ART, namely IVF or ICSI. Results: Using a multivariate logistic regression analysis mode, there is a higher prematurity rate in twin pregnancies OR 16 (95% CI 10.7, 23.8), donor conception OR 1.8 (95% CI 1.1, 3.3) and PIH pregnancy OR 2.6 (95% CI 1.5, 4.5). The odds of malformations in these ART pregnancies are increased by the stage of the embryo (day 3) OR 2.6 (95% CI 1.3, 5.2), fresh embryo transfer OR 2 (95% CI 1.2, 3.4) and donor conception OR 2.3 (95% CI 1.2, 4.4). The ART used (IVF/ICSI) does not influence the prematurity or birth defects rate. Conclusions: Donor conception is found to increase the odds of both prematurity and congenital malformations. The ART used (IVF/ICSI) does not influence the prematurity or birth defects rate.