Obesity is one of the biggest public health problems today because obese people have an increased risk of developing a number of severe chronic diseases. Several monogenic mutations associated with obesity are known, but in most individuals obesity has a complex background. The leptin receptor, encoded by the LEPR gene, binds to the hormone leptin, which signals a feeling of satiety, and ghrelin is a hormone that stimulates the feeling of hunger. In this paper, the frequencies of alleles and genotypes of rs1805094 variants of the LEPR gene and rs35683 of the GHRL gene in three Roma populations in Croatia (n = 440) were analyzed and their association with anthropometric indicators of overweight and obesity was examined. The Roma population is characterized by a high prevalence of obesity, and their evolutionary past by several founding effects and a high degree of endogamy. The frequencies of genotypes and alleles of the rs1805094 polymorphism did not differ between the three Roma populations, while the frequencies of genotypes of the rs35683 polymorphism differed significantly; compared to the population of Baranja and Zagreb, there were significantly more heterozygotes in MeĎimurje. 28.08% of population was obese; women and men alike, while there were 3x more malnourished women than men (6.6% vs. 1.9%). Compared to other regions and people of the same sex, Roma from Zagreb were more often obese and more often had an increased abdominal circumference, and the least obese Roma women were in MeĎimurje. Carriers of the rs35683 CC genotype had the highest mean values of body mass index and some other anthropometric indicators of excess weight. The rs1805094 polymorphism did not show an association with anthropometric characteristics of the Croatian Roma population.