Background and Objectives  Autologous peripheral blood stem cell transplantation has recently become a standard therapeutic approach to virus‐related or infected haematological malignancies. Collection, manipulation, storage and thawing of leukapheresis products in this subset of patients require strict monitoring to prevent infection risk for operators and risk of contamination for other stored bags. Materials and Methods  This is a non‐randomized retrospective observational study. In the 2000–2002 period, a single bag freezing procedure was used for autologous peripheral blood stem cell transplantation. Bags were stored in tanks containing liquid and gas phase nitrogen. In 2002, the processing procedure was revised, and a second additional safety bag and a new storage tank containing jacketed liquid nitrogen have been used. Results  A total of 524 bags were thawed, of which 121 processed with the single bag method and 403 with the double bag method. Forty‐nine and 109 patients were infused respectively. The observed rupture rate with the single bag in liquid and gas phase nitrogen was 17 and 2·5%, respectively, against a rupture rate as little as 0·24% with the new methodology. Viability revealed levels of 84·4% ± 6·1% and 96·9% ± 2·4% for the single and double‐bag respectively. This statistically significant (P < 0·0001) difference correlated with better neutrophil engraftment. Conclusions  The new proposed method, based on a double bag and storage freezer without liquid or gas phase nitrogen into a cryogenic chamber, significantly reduces bag rupture and bio‐hazard and improves stem cell viability and neutrophil engraftment remarkably.