Follicular cysts are an important disorder affecting 5 to 30% of dairy cows that leads to abnormal estrous cycle behavior and economic losses due to infertility. The aim of this study was to compare the mRNA expression in follicular cells of cows classified either as having a follicular cyst or cycling with dominant follicle (DF). Lactating dairy cows (n = 22) were examined weekly by ultrasound and 11 cows (Holstein, n = 7; Jersey n = 3; and Shorthorn n = 1) were classified as having a follicular cystic (CYS, follicle >25 mm with absence of corpus luteum) whereas 11 cows (Holstein, n = 11) were classified as cycling with a dominant follicle (CON, presence of corpus luteum and dominant follicle, n = 11). Cows were at 94.4 (30 – 382) DIM, milk yield 37.9 ± 12 kg /d, and parity 2.6 ± 1.3. Cows in CON had follicle diameter of 14.10 ± 3 mm whereas cows in CYS had follicle diameter of 35.73 ± 10.2 mm. Follicular fluid from each cow was aspirated and follicular cells were retrieved immediately by centrifugation, frozen in liquid nitrogen and stored at −80°C until RNA extraction. The mRNA expression for LHCGR, STAR, 3β-HSD, P450scc, CYP19A1, IRS1, IGF, TLR4, TNF, IL1- β, IL8 and IL6 was measured by real-time PCR. Statistical analysis was performed using the MIXED procedure of SAS. LHCGR, 3β-HSD, CYP19A1, IRS1 mRNA expression was higher (P < 0.05) in CON (1.37 ± 0.4, 5.58 ± 1.2, 1.33 ± 0.2, 1.41 ± 0.3, respectively) than CYS (0.69 ± 0.3, 3.24 ± 0.9, 0.24 ± 0.01, 0.74 ± 0.2, respectively) with breed effect (P < 0.07). Expression of mRNA for IGF, TLR4, TNF and IL8 was lower (P < 0.05) in CON (0.55 ± 0.07, 0.61 ± 0.2, 0.54 ± 0.3, 0.12 ± 0.01, respectively) than in CYS (4.62 ± 0.7, 3.40 ± 0.5, 1.58 ± 0.3, 0.52 ± 0.04, respectively), with no breed effect (P > 0.20). There was no difference (P > 0.05) for STAR, P450scc, IL6 and IL1-β mRNA expression between CYS and CON. In conclusion, cows in CYS had lower expression of genes related to steroidogenesis and energy metabolism and greater expression of genes related to inflammation than CON. It seems that an inflammatory response may be involved in the follicular cyst etiology.