Background <p>The early diagnosis of odontogenic cysts is crucial to prevent future complications and to choose an effective treatment plan. Dentigerous cysts (DCs) and odontogenic keratocysts (OKCs) are two common developmental cysts that affect the jaw. OKCs show locally aggressive behavior and a higher recurrence rate compared with DCs, emphasizing the need for reliable molecular diagnostic markers. MicroRNAs (miRNAs) are abnormally expressed in tumors and lesions with aggressive behavior and have potential as adjunctive biomarkers. This study investigates the diagnostic potential of miR-221, miR-214, and miR-375 expression in OKCs and DCs, due to the invasive nature of OKCs compared with DCs.</p> Materials and methods <p>This study analyzed 36 paraffin-embedded odontogenic cyst tissue samples (23 OKC and 13 DC) collected from the oral pathology archive of Islamic Azad University. Total RNA, including miRNAs, was extracted using TRIzol-based protocols with RNase-free conditions. RNA purity and integrity were assessed via spectrophotometry and agarose gel electrophoresis. Reverse transcription was performed using the M-MLV RNase H kit. Specific primers for miR-221, miR-214, and miR-375 were designed and verified. Quantitative real-time PCR was conducted using SYBR Green, and delta cycle threshold (ΔCt) values were calculated.</p> Results <p>miR-221, miR-214, and miR-375 showed significantly lower ΔCt values in OKCs compared with DCs (<i>p</i> &lt; 0.001). The mean ΔCt values for miR-221, miR-214, and miR-375 in OKCs were 11.27, 10.10, and 8.18, respectively, compared with 12.95, 12.51, and 11.05 in DCs.</p> Conclusion <p>The ΔCt values for miR-221, miR-214, and miR-375s were significantly lower in OKC samples, indicating higher expression levels compared with DCs. The significant upregulation of these miRNAs in OKCs compared with DCs suggests that these miRNAs may indicate predictive roles and could serve as supportive biomarkers.</p>