Introduction. Freezing of ovarian tissue is used for preservation of fertility. The freezing-thawing process is accompanied by oxidative stress and induction of apoptosis. Apoptosis is a complex process that has been studied in animal models. The present study was aimed at investigating the effect of selenium on suppression of apoptosis during vitrification-thawing process of mice ovary via studying expression of apoptosis-related genes, and also, we aimed to design statistical models for the roles of single genes and gene-gene interactions in suppression of apoptosis. Methods. A total of 10 right ovary samples from 10 mice were randomly divided into two groups of selenium treatment (at dose 5 μg/ml sodium selenite, through adding to the media) and control group. Vitrification-thawing process was done according to the existed protocols. Real-time PCR was used for gene expression study. The apoptosis gene profile included P53, Bax, Fas, and Bcl-2. General linear model was applied to study single gene associations and gene-gene interactions. Results. From the studied genes, P53 showed a significant downregulation in the selenium group in comparison to the control group (∆∆CT=1.96; P=0.013; relative expression RE=0.28). Bcl-2 showed a significant upregulation in the selenium group in comparison to the control group (∆∆CT=−2.49; P<0.001; RE=3.49). No significant result was found for other genes. According to the multiple models, Bcl-2 showed a protective single gene association (beta=−0.33; P=0.032), and Fas∗Bcl-2 interaction was significantly positive (beta=0.19; P=0.036). Conclusion. Addition of selenium to cryomedia of vitrification-thawing process could reduce the apoptosis induced by freezing-thawing stress in mice ovary via downregulation of P53 and upregulation of Bcl-2 at transcription level. Multivariable statistical models should be performed in future researches to study biological systems.