Objective: analyzing the perceptions of nurses about the clinical pain in neonates in neonatal intensive care unit. Method: a descriptive, exploratory study, of a qualitative approach conducted with ten nurses in the neonatal intensive care unit of the University Hospital Antônio Pedro applying a semi-structured interview for data collection, and analyzed according to thematic content analysis method. Results: understanding the mechanism of neonatal pain, which does not depend upon complete formation of myelination; lack of verbalization of the newborn and this fact complicates the assessment of pain; however we must be sensitive to other physiological and behavioral signs, such as: facial mimicry, heart and respiratory rate, systolic blood pressure, oxygen saturation, palmar sweating and vagal tone. Conclusion: it is a practice to be rethought the use of protocols and scales for the evaluation of indicators of neonatal pain