1. All lysine residues in native troponin I from rabbit fast-twitch skeletal muscle reacted with methyl acetimidate and ethyl acetimidate. 2. The reactivity of lysine-18 of troponin I to acetimidate was much diminished when the troponin I was complexed in the presence of Ca2+ with troponin C alone or in the whole troponin complex. 3. In the presence of EGTA, lysine-18 of troponin I in the troponin I-troponin C complex was more reactive to acetimidate than it was in the presence of Ca2+. 4. No masking of lysine residues could be detected when troponin I interacted with calmodulin or actin. 5. Sedimentation-equilibrium studies indicated that the complex of troponin I with calmodulin was more readily dissociated in the absence of Ca2+ than was its complex with troponin C under otherwise identical conditions. 6. These studies suggest that the nature of the involvement of the N-terminal region of troponin I is a major difference between its modes of interaction with calmodulin and with troponin C.