Main objective of the study was to assess the nutritional status of school age Roma children in Macedonia in order to detect precursors of possible health risks at an early age. The study was designed as a comparative case control study. Study group consisted of 229 Roma school children from the 1st and 272 from the 5th grade residing in different towns in Macedonia. The control group was recruited from other than Roma ethnic background and consisted of 283 children attending 1st and 356 children attending 5th grade. Every participant was measured for his/hers body height and weight. The t-test and Chi square (Chi2) were applied to test statistical significance of variables. The WHO's AnthroPlus software was applied to assess growth parameters and population at risk. There were significant differences in values of the body weight (p = 0.001) and height (p = 0.001) between Roma and non-Roma children attending the 1st grade of primary school. Weight-for-age, height-for-age and BMI-for-age indexes of the 1st grade children significantly differred in in the same intervals of SD (> or = -2SD and < -1SD; > or = -1SD and median; > +1SD and < or = +2SD; between Roma and non-Roma 5th graders. Anthropometric parameters of nutritional status of Roma children in Macedonia are significantly different than those of their non-Roma peers. Their health risks are predominantly related to underweight. The parameters related to health risks of overweight or obesity are lower in Roma than in non-Roma children.