We report on the search for Strange Quark Matter (SQM) and charged Q-balls with the SLIM experiment at the Chacaltaya High Altitude Laboratory (5230 m a.s.l.) from 2001 to 2005. The SLIM experiment was a 427 m 2 array of Nuclear Track Detectors (NTDs) arranged in modules of 24 × 24 cm 2 area. SLIM NTDs were exposed to the cosmic radiation for 4.22 years after which they were brought back to the Bologna Laboratory where they were etched and analyzed. We estimate the properties and energy losses in matter of nuclearites (large SQM nuggets), strangelets (small charged SQM nuggets) and Q-balls; and discuss their detection with the SLIM experiment. The flux upper limits in the CR of such downgoing particles are at the level of 1.3 × 10 −15 cm −2 s −1 sr −1 (90% CL).