Comparative histopathological study and analysis of parasite load in different muscle groups were carried out in BALB/c mice during the acute phase of Chagas disease. Activities of C104 clone of T. cruzi strain TPAP/MX/2002/Albarrada and the parental strain were compared. Panoramic 2D-microscopy imaging of sample surface was used and quantitative analysis of parasitism and pathologic damage was performed. The infection rates in various muscle groups were as follows: myocardium=abdominal muscles=lumbar muscles=femoral muscles<--diaphragm for the clone and myocardium¬abdominal muscles=lumbar muscles=femoral muscles-->diaphragm for the parental strain.