Introduction: Overuse of antibiotics has been increasing in recent years and is currently the most prescribed drug in the paediatric age. It is estimated that 72% of patients in the neonatal intensive care unit (NICU) are treated with antibiotics. One of the effects observed with their use is the alteration of the microbiota, which is associated with metabolic disorders including obesity. In this study, the aim was to determine in newborn rats, whether most commonly prescribed antibiotics in Mexican NICUs have a differential effect on weight gain, development of adiposity, and modification of carbohydrate and lipid metabolism. Methods: This is an experimental study in newborn rats, comparing Ampicillin/Meropenem (Access/Watch groups) 100 mg/g every 12 h /10 mg/g every 12 h (each of these two antibiotics was adjusted to the required dosages based on weight); Cefotaxime 200 mg/g every 24 h; (Watch group) and Amikacin 15 mg/g every 24 h (Access group) versus Saline Solution as Control. Each antibiotic was intraperitoneal administered daily for 5 days in males (to avoid gender differences) to 14 newborn rats in each group. A comparison of anthropometric and biochemical parameters registered on day 28 was made using ANOVA analysis. Differences were considered if p < 0.05.Results: Amikacin was the antibiotic with the greatest effect on anthropometric measurements and LDL-cholesterol; as well as Cefotaxime on Glucose and triglycerides, while Meropenem plus Ampicillin showed the weakest effect on measured parameters. Conclusion: The administration of antibiotics in the neonatal stage has repercussions on the body composition of adult rats, as well as on lipids and carbohydrates serum levels. Future studies might evaluate the toxicity of antibiotics on the immature neonatal organs.