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Background. Drugs of abuse could interfere with the hypothalamic-pituitary-gonadal axis, causing impaired functions of the gland and associated functions of target organs. Drugs of abuse tend to cause changes in the endocrine system, and these changes could be physiological, molecular, biochemical, genetic, and cellular. Method. A case-control study design was conducted from a total of 171 male consented study participants (148 drug abusers and 23 controls). The serum gonadal and cortisol hormone levels were assayed using the electrochemiluminescence immunoassay method. Socio-demographic variables were collected using a semi-structured questionnaire by the interview method. Nonparametric statistical tools (Mann–Whitney test and median) were used to compare the groups. In all cases, P<0.05 was considered statistically significant. Result. The median age for drug abusers and control groups was 27, and the age difference between drug abusers and control group was not statistically important. The median estradiol levels among chronic khat chewers (39.4 pg/ml), marijuana (44 pg/mL), and users of heroin (40.2 pg/mL) were significantly higher than control groups (23 pg/mL), P<0.003. However, the median luteinizing hormone levels among chronic khat chewers (5 IU/L), marijuana users (5 IU/L), and heroin users (5.6 IU/L) were significantly lower than those of control groups (6.2 IU/L), P<0.02. The median testosterone levels among chronic khat chewers (6.1 ng/mL), marijuana users (6.3 ng/mL), and heroin users (6.6 ng/mL) were significantly lower than control groups (8.0 ng/mL), P<0.003. However, cortisol and follicle stimulating hormone did not show statistically significant difference between users of khat, marijuana, and heroin compared with the control group. Conclusion. The drug abuser group had significantly lower testosterone and luteinizing hormone levels compared with control groups. Drug abuse has been shown to affect gonadal hormones in an unusual physiological phenomenon. These findings reveal the need for intervention programs to solve these problems.