We analyze the effect of microscopic disorder on the macroscopic properties of composite metamaterials and study how weak statistically independent fluctuations of the parameters of the structure elements can modify their collective magnetic response and left-handed properties. We demonstrate that even a weak microscopic disorder may lead to a substantial modification of the metamaterial magnetic properties, and a 10% deviation in the parameters of the microscopic resonant elements may lead to a substantial suppression of the wave propagation in a wide frequency range. A noticeable suppression occurs also if more than 10% of the resonant magnetic elements possess strongly different properties, and in the latter case the defects can create an additional weak resonant line. These results are of a key importance for characterizing and optimizing novel composite metamaterials with the left-handed properties at terahertz and optical frequencies.