Fine needle aspiration cytology (FNAC) plays a pivotal role in evaluating salivary gland (SG) tumors. Several studies have shown diagnostic utility of MILAN system for reporting salivary gland cytopathology (MSRSGC) by examining risk of malignancy but only an occasional study has focused on interobserver variability. Hence, the present study was undertaken to assess the agreement among cytopathologists with varying experience in SG cytopathology using MSRSGC and to re-evaluate discordant cytohistological diagnoses for possible causes of misinterpretation. All SG lesions subjected to FNAC over a period of 3½ years were studied. The cases were critically reviewed by 2 pathologists with variable experience in cytopathology using MSRSGC and concordance level among them was calculated. Cytohistological discordant diagnoses were reclassified and possible causes of misinterpretation during routine reporting were evaluated. Of 150 SG aspirates categorized according to MSRSGC, diagnostic disagreement between 2 pathologists was found in 10. Unweighted Cohen's Kappa score between consultant and resident was 0.812 (high). Among 55 cases with histological correlation, cytohistological discordance was seen in 12. True pitfalls constituted 50% of discordant cases while rest 50% were attributed to practical issues (turnaround time and heavy case load) during routine reporting. MSRSGC can be used with good reproducibility between observers with variable cytopathology experience. Heterogeneous nature of SG neoplasm is a known pitfall in FNA diagnosis of SG neoplasms. During routine reporting turnaround time, heavy case load and reporting by cytopathologists with variable experience add on to challenges faced in reporting cytopathology of SG neoplasm.