Laryngeal muscles are specialized for fine control of voice, speech, and swallowing, and may differ from limb muscles in many aspects. Because muscles and their controlling motor neurons communicate via neuromuscular junctions (NMJs), we hypothesized that NMJs in laryngeal muscles have specialized characteristics different from limb muscles. In vivo study. Single muscle fibers from 12 Sprague-Dawley rats (six male, six female) were used to analyze the postsynaptic side of NMJs from laryngeal thyroarytenoid (TA), cricothyroid (CT), posterior cricoarytenoid (PCA), limb soleus (SOL), and extensor digitorum longus (EDL) muscles. NMJs were labeled with rhodamine-conjugated α-bungarotoxin. With confocal microscopy, we counted cluster fragments and measured the NMJ area, both absolute and normalized (corrected by muscle fiber diameter), for at least 10 single fibers from each muscle of each animal. Differences between genders were also compared. Cluster fragments of postsynaptic NMJs were more numerous in PCA and TA compared to CT, SOL, and EDL muscles (P < .01) in both male and female rats. NMJ cluster fragments were more numerous in female than in male rats only in the TA muscle (P < .01). The absolute area covered by the NMJs showed SOL > EDL > PCA > CT > TA (P < .01); however, with normalization the SOL = EDL = PCA > CT = TA. Differences found in NMJ surface and organization between laryngeal and limb muscle fibers may relate to specialized laryngeal muscle functions. Differences in NMJs between male and female rats were found only in the TA muscle, suggesting an underlying mechanism for some gender-specific laryngeal disorders related to abnormal TA muscle activity.