To investigate the expression and signification of B-cell lymphoma/leukemia-2 (bcl-2), bax and ER proteins in epithelial cells in different depth of adenomyosis. Expression and correlation of bcl-2, bax and ER proteins were detected by immunohistochemistry staining in 36 adenomyosis cases with superficial (< 1/2 depth of penetration) and deep (≥ 1/2 depth of penetration) ectopic endometrium and eutopic endometrial tissues matched with 30 cases with benign ovarian tumor, uterine septum, pelvic floor dysfunction without adenomyosis as controls. (1) The expression of ER protein in superficial and deep ectopic tissues (5.04 ± 0.24, 4.91 ± 0.16) were found significantly lower than 6.06 ± 0.36 in eutopic tissues (P < 0.01) and higher than 3.70 ± 0.58 in control group (P < 0.05). There was no statistical difference of ER expression in superficial and deep ectopic endometrium (P > 0.05). (2) The level of bcl-2 protein of 5.6 ± 0.4 in superficial and 6.0 ± 0.3 in deep myometrium of ectopic tissues were significantly higher than 3.6 ± 0.4 in eutopic tissues and 1.9 ± 0.4 in control group (P < 0.01). (3) The level of bax protein of 3.50 ± 0.28 in superficial and 4.80 ± 0.29 in deep myometrial ectopic and 4.43 ± 0.37 in eutopic tissues were significantly lower than 6.18 ± 0.65 in control groups (P < 0.05). The expression of bax in superficial myometrium is significantly lower than deep myometrium in ectopic tissues (P < 0.01). (4) The positive correlation between the expression of ER and bcl-2 protein at superficial myometrium of ectopic tissues (r = 0.720, P < 0.01). And there was no significant correlation with the expression of ER and bax protein at superficial myometrium (r = 0.008, P > 0.05). As well as, there was not significant correlation with the expression of bcl-2, bax and ER protein at deep myometrium (r = 0.089, r = -0.023, P > 0.05). The expression of bax protein in ectopic endometrium was positive correlation with the depth of adenomyosis penetration (r = 0.736, P < 0.01). There was positive correlation between the expression of ER and bcl-2 protein at normal endometrium (r = 0.453, P < 0.05). And there was negative correlation between the expression of ER and bax protein at control group (r = -0.514, P = 0.05). The bax protein expression of ectopic endometrium in deep adenomyosis was higher than superficial adenomyosis.