Myokines are cytokines secreted by muscle and exert autocrine, paracrine, or endocrine effects. Myokines mediate communication between muscle and other organs, including adipose tissue. The aim of the study was to assess serum myokines and their relationships with adipokines and anthropometric and nutritional parameters in children following vegetarian and omnivorous diets. One hundred and five prepubertal children were examined. Among them there were 55 children on a vegetarian diet and 50 children on an omnivorous diet. Concentrations of myokines (myostatin, irisin) and adipokines (leptin, adiponectin, omentin, visfatin) in serum were determined by enzyme-linked immunosorbent assay (ELISA). We observed comparable median values of serum myokines and adipokines (except of leptin concentration) in both of the studied groups of children. We also found several correlations between myokine and adipokine levels and certain nutritional parameters. Serum myostatin was positively correlated with omentin levels in vegetarians and omnivores (p = 0.002). Serum irisin was positively associated with omentin (p = 0.045) levels in omnivores and inversely with visfatin concentration (p = 0.037) in vegetarians. Myostatin concentration was negatively correlated with the percentage of energy from protein (p = 0.014), calcium (p = 0.046), and vitamin A (p = 0.028) intakes in vegetarians and with dietary vitamin C (p = 0.041) and vitamin E (p = 0.021) intakes in omnivores. In multivariate regression analyses, positive correlations of serum myostatin with omentin levels were revealed in both study groups (β = 0.437, p < 0.001 for vegetarians; and β = 0.359, p = 0.001 for omnivores). Consuming a lacto-ovo-vegetarian diet did not influence serum levels of myokines (myostatin, irisin) and adipokines such as adiponectin, visfatin, and omentin in prepubertal children. However, leptin levels were significantly lower in vegetarians compared with omnivores. The observed significant positive correlations between myostatin and omentin concentrations might suggest tissue cross-talk between skeletal muscle and fat tissue. Further studies, carried out in a larger group of children following different dietary patterns, could be important to fully understand the relations between muscle, adipose tissues, and nutrition.