Background: Nowadays, parents are paying more attention to the penis size of their children, especially obese children. Objectives: The aim of this study was to investigate the correlation between obesity, testosterone, and estradiol in prepubertal non-obese and obese children with micropenis. Methods: This case-control study was done on 58 non-obese and 86 obese micropenis children aged 8-13 years at Golestan Hospital, Tehran, Iran, from June 2018 to May 2020. The body mass index (BMI), testosterone and estradiol levels, stretched penile length (SPL), and the correlation between these were studied. Results: The mean age of children in non-obese and obese groups was 10. 2 1. 34 and 10. 5 1. 6 years, respectively. SPL in nonobese and obese subjects was 3. 1 1. 3 and 2. 9 1. 22 cm, respectively. SPL in both groups was significantly correlated with height and testosterone (height: r = 0. 239, P = 0. 009; testosterone: r = 0. 344, P = 0. 001) but not with BMI, weight, and estradiol. After the adjustment for age, BMI, weight, and estradiol, adjusted odds ratio with confidence interval 95% for penile length across to height and testosterone levels in non-obese group was 1. 52 (0. 91-1. 83; P = 0. 001) and 0. 56 (0. 36-0. 98; P = 0. 001), respectively and in the obese group was 1. 42 (0. 81-1. 66; P = 0. 001) and 0. 75 (0. 51-0. 87; P = 0. 001), respectively. Conclusions: Penile length is positively correlated with height and testosterone but not with weight and estradiol in non-obese and obese children. It is probably not essential and obligatory to recommend weight loss for this issue and weight loss should not be concerned by children and their parents.