Radiofrequency (RF) catheter ablation in the septal arrhythmia substrates has an increased risk of irreversible atrioventricular block. Despite its safety profile, several studies reported a lower acute success rate and a higher recurrence rate with cryoablation of septal accessory pathways (APs) when compared to RF ablation. The aim of this study was to assess the efficacy and safety of cryoablation of right septal APs using an electroanatomical mapping system guidance. A total of 43 consecutive patients (13.2 ± 5.5 years) underwent cryoablation for right septal APs. The EnSite system (St. Jude Medical, St. Paul, MN, USA) was used in all procedures. No fluoroscopy was used in 90% of patients (39/43). The mean fluoroscopy time in the remaining four patients was 3.7 ± 0.7 minutes. An electrophysiology catheter with 2-mm distal spacing was used to determine the precise AP location. The majority of the patients (20/43) had anteroseptal, and remaining of the patients had posteroseptal (15/43) and midseptal (8/43) APs. A 6-mm-tip catheter was used in 33 patients and 8-mm-tip catheter was used in nine patients (both catheters were used in one patient). The mean procedure duration and number of complete cryoablation lesions were 181.5 ± 60.6 minutes and 6.1 ± 3.1 minutes, respectively. Acute success was achieved in 40 of 43 patients (93%). No complications were noted. During a mean follow-up of 8.8 ± 4.8 months, five patients (12.5%) experienced recurrence. Our data suggest that cryoablation of septal APs can be performed safely with comparable efficacy to the reported RF ablation results using a limited fluoroscopy approach.