(1) Background: The effects of serum vitamin D levels, the vitamin D receptor (VDR), and phosphohistone H3 (PHH3) in endometriosis were investigated in two cohorts of women with this pathology: those receiving hormonal treatment and those without treatment. (2) Methods: In 60 cases of women with endometriosis (26 with progestin treatment and 34 without), paraffin-embedded endometriosis tissue samples retrieved after surgery were immunohistochemically (IHC) analyzed to determine the expression statuses of VDR and PHH3. In addition, serum levels of 25(OH) vitamin D were assessed for each patient. (3) Results: The serum 25(OH) vitamin D evaluations revealed higher levels of 25(OH) vitamin D in women with treatment compared with those without. The positive IHC indexes of VDR and PHH3 in these two groups were compared. Vitamin D receptor levels were positively correlated with PHH3 levels, both being increased in patients without treatment. (4) Conclusions: Serum 25(OH) vitamin D levels and IHC analysis of VDR and PHH3 can be used as additional tools for risk stratification and prognostic assessment in patients with endometriosis.