The present study examines the effects of protein- and energy-type malnutrition in combination with Zn deficiency on the growth, serum insulin-like growth factor-1 (IGF-1), gastrocnemius muscle mass and fibre diameter of growing rats during a deficiency phase followed by nutritional rehabilitation. Rats (3-weeks old) were randomly assigned to baseline, or Zn-deficient (Z, < 1 mg Zn/kg), protein-deficient (P, 20 g protein/kg), combined Zn- and protein-deficient (ZP), energy-deficient (E, feed intake pair-fed to Z) or control (C, 30 mg Zn/kg and 170 g protein/kg) groups for a 3-week deficiency phase, followed by a 3-week repletion phase with the control diet. ATPase histochemical staining at pH 9·4 was used to differentiate type 1 and type 2 muscle fibres. After the deficiency phase, the ZP and P groups had lower body weight and smaller gastrocnemius muscle mass than the Z and E groups. Type 1 and 2 muscle fibre diameters (T1- and T2-MFD, respectively) were reduced in the ZP, P and Z groups compared with the E and C groups. Serum Zn was reduced in the ZP, P and Z groups, but serum IGF-1 was lowest in the Z and E groups. After the repletion phase, T1-MFD did not recover in the P and E groups nor T2-MFD in the P group, despite the P and E groups having a better recovery of body weight. In summary, previous protein deficiency, but not Zn deficiency, limited the recovery of both T1- and T2-MFD during nutritional repletion. The quality of skeletal muscle recovery in the malnourished groups was not associated with body weight, muscle mass, serum Zn or IGF-1 concentrations.