To test the hypothesis that irradiated volume of specific subregions of pelvic active bone marrow as detected by (18)FDG-PET may be a predictor of decreased blood cells nadirs in anal cancer patients undergoing concurrent chemoradiation, we analyzed 44 patients submitted to IMRT and concurrent chemotherapy. Several bony structures were defined: pelvic and lumbar-sacral (LSBM), lower pelvis (LPBM) and iliac (IBM) bone marrow. Active BM was characterized employing (18)FDG-PET and characterized in all subregions as the volume having standard uptake values (SUVs) higher than SUVmean. All other regions were defined as inactive BM. On dose-volume histograms, dosimetric parameters were taken. Endpoints included white blood cell count (WBC), absolute neutrophil count (ANC), hemoglobin (Hb) and platelet (Plt) nadirs. Generalized linear modeling was used to find correlations between dosimetric variables and blood cells nadirs. WBC nadir was significantly correlated with LSBM mean dose (β = -1.852; 95 % CI -3.205/-0.500; p = 0.009), V10 (β = -2.153; 95 % CI -4.263/-0.721; p = 0.002), V20 (β = -2.081; 95 % CI -4.880/-0.112; p = 0.003), V30 (β = -1.971; 95 % CI -4.748/-0.090; p = 0.023) and IBM V10 (β = -0.073; 95 % CI -0.106/-0.023; p = 0.016). ANC nadir found to be significantly associated with LSBM V10 (β = -1.878; 95 % CI -4.799/-0.643; p = 0.025), V20 (β = -1.765; 95 % CI -4.050/-0.613; p = 0.030) and IBM V10 (β = -0.039; 95 % CI -0.066/-0.010; p = 0.027). Borderline significance was found for correlation between Plt nadir and LSBM V30 (β = -0.056; 95 % CI -2.748/-0.187; p = 0.060), V40 (β = -0.059; 95 % CI -3.112/-0.150; p = 0.060) and IBM V30 (β = -0.028; 95 % CI -0.074/-0.023; p = 0.056). No inactive BM subsites were found to be correlated with any blood cell nadir. (18)FDG-PET is able to define active bone marrow within pelvic osseous structures. LSBM is the strongest predictor of decreased blood cells nadirs in anal cancer patients undergoing concurrent chemoradiation.