Background During erythropoietin-stimulating agent (ESA) treatment, hemoglobin (Hb) levels usually fluctuate; this phenomenon is known as “Hb cycling (HC).” In this study, we aimed to evaluate the predictors of HC and its impact on left ventricular hypertrophy (LVH) as a patient-important outcome parameter in pediatric dialysis patients. Methods Records of patients followed up in nine pediatric nephrology centers between 2008 and 2013 were reviewed. More than 1 g/dL decrease or increase in Hb level was considered as HC. Patients were divided into two groups according to 12-month Hb trajectory as rare cycling (RC) (≤ 3) and frequent cycling (FC) (> 3 fluctuation) as well as three groups based on T-A-Hb levels: < 10, 10–11, and > 11 g/dL. Results Two hundred forty-five dialysis (160 peritoneal dialysis (PD) and 85 hemodialysis (HD)) patients aged 12.3 ± 5.1 (range 0.5–21) years were enrolled in this study. Fifty-two percent of the patients had RC, 45% had FC, and only 3% had no cycling. There were no differences between HC groups with respect to age, dialysis modality, having anemia, hospitalization rate, residual urine volume, and mortality. Although left ventricular mass index (LVMI) tended to be higher in RC than FC group (65 ± 37 vs 52 ± 23 g/m 2.7 , p  = 0.056), prevalence of LVH was not different between the groups ( p  = 0.920). In regression analysis, FC was not a risk factor for LVH, but low T-A Hb level (< 10 g/dL) was a significant risk for LVH (OR = 0.414, 95% CI 0.177–0.966, p  = 0.04). The target Hb levels were more often achieved in PD patients, and the number of deaths was significantly lower in non-anemic patients (Hb level > 11 g/dL). Conclusion Hb cycling is common among dialysis patients. Severity of anemia rather than its cycling has more significant impact on the prevalence of LVH and on inflammatory state.