Undiagnosed and untreated celiac disease (CD) constitutes an increasing skeletal health problem due to its association with low bone density and fractures. Examinations of skeletal status in children using dual-energy X-ray absorptiometry (DXA) are prone to size-related misinterpretation. In contrary, the analysis of muscle-bone relationship seems to limit a possibility of misdiagnosis because skeletal status is evaluated from the functional perspective. The study was aimed to assess skeletal status of children suffering from CD with the use of muscle-bone functional algorithm. The study group comprised 29 celiac patients (13.7yr+/-2.9) on gluten-free diet (GFD), and 24 newly diagnosed atypical celiac patients, including subgroup with normal height (n=14; 12.6yr+/-3.9) and subgroup with short stature (n=10; 12.2yr+/-2.9). Muscular and skeletal status was evaluated by DXA (DPX-L, GE). Anthropometry, total body bone mineral density (TBBMD, g/cm(2)). and total body bone mineral content (TBBMC, g) as well as lean body mass (LBM, g) were evaluated. Muscle-bone interactions were estimated using TBBMC/LBM ratio. Previously established references for healthy controls were used for the calculation of Z-scores (age-matched) and SD-scores (height-matched). GFD treated celiacs and atypical celiacs with normal body height had TBBMD, TBBMC, LBM, and TBBMC/LBM ratio Z-scores and SD-scores within normal range for healthy controls. In contrary, atypical celiacs with short stature had significantly lower Z-scores for TBBMD (-2.3+/-0.4), TBBMC (-2.1+/-0.3), LBM (-1.4+/-0.3). and TBBMC/LBM ratio (-2.3+/-0.6) when compared to respective values observed in GFD treated celiacs (p<0.001, p<0.001, p<0.05, p<0.01) and atypical celiacs with normal height (p<0.01, p<0.01, p<0.05, p<0.01). When body-height matching of DXA data was used to limit the influence of body size, the atypical celiacs with short stature had SD-scores for TBBMD (-1.3+/-0.7), TBBMC (-1.3+/-0.6), and LBM (+0.8+/-0.3) not significantly different from the corresponding SD-scores obtained in the remaining 2 groups. Nevertheless, short stature in atypical celiacs still coincided with significantly lower TBBMC/LBM ratio SD-score of -1.9+/-0.7 when compared to values observed in GFD treated celiacs (+0.04+/-0.2; p<0.05) and atypical celiacs with normal height (-0.4+/-0.2; p<0.05). GFD regime in classic celiacs corresponded with physiological values of DXA assessed indicators of bone and muscle status as well as normal muscle-bone interactions. Untreated atypical celiacs may present a broad spectrum of heterogeneous abnormalities from normal to markedly depressed TBBMC/LBM ratio values pointing on the marked imbalance between TBBMC and LBM.