Background and Objectives: Fine needle aspiration cytology (FNAC) is an established out- patient procedure used in primary diagnosis of palpable thyroid lesions. A modified technique fine needle capillary sampling (FNCS) obviates the need of suction, is less painful, patient friendly and reported to overcome the problem of inadequate and bloody specimens. The aim of our study was to compare the efficacy and quality of FNCS with that of conventional FNAC in the lesions of thyroid. Methods: One hundred patients, presenting between January 2011 to December 2012 at Cytopathology Department of M M Institute of Medical Sciences and Research, Mullana, with diffuse and nodular thyroid lesions were enrolled with both the techniques being executed on the patients, beginning with FNA followed by FNCS. The smears were scored using five objective parameters i.e. background blood, cellular material, cellular degeneration, cellular trauma, and retention of appropriate architecture, in a single blind setting by a cyto-pathologist. The results were analyzed using Student’s test for paired data and chi- square analysis. Results: A highly significant differences (P<0.001) in favor of FNCS was observed for the background blood, cellular material and retention of architecture while total score favored FNA for cellular degeneration and degree of cellular trauma. Total scores and average score per case for FNCS was significantly better (P<0.001) than FNA. FNCS technique yielded more diagnostically superior and lesser number of unsatisfactory smears whereas greater number of diagnostically adequate samples was obtained by FNA technique. Conclusion: FNCS offers more number of diagnostically better quality smears. Both techniques could be supplementary on many occasions and substitutive on a few. Combination of the two techniques could offer better diagnostic accuracy.