An experiment was conducted to test the hypothesis that values for apparent total tract digestibility (ATTD) of Ca in pigs are influenced by endogenous Ca lost from the gastrointestinal tract. The objective was to determine the endogenous loss of Ca, the ATTD of Ca, and the true total tract digestibility (TTTD) of Ca in canola meal without and with microbial phytase. The second objective was to determine the balance of Ca in pigs fed diets based on canola meal without or with microbial phytase. Forty-eight growing barrows (initial BW: 16.72 ± 2.52 kg) were allotted to 8 dietary treatments in a randomized complete block design with 6 pigs per treatment. Diets were based on sucrose, cornstarch, potato protein isolate, corn gluten meal, and canola meal. Diets were formulated to contain 0.08, 0.16, 0.24, or 0.32% Ca from canola meal. All diets were formulated with 0 or 1,500 units/kg of microbial phytase and contained 0.32% digestible P. Feces and urine samples were collected from d 6 to 11. Total endogenous losses of Ca were determined using the regression procedure. Results indicated that ATTD of Ca and Ca retention increased (P < 0.05) if dietary Ca increased and also increased (P < 0.01) when phytase was added to the diets. The estimated total endogenous loss of Ca was 0.160 and 0.189 g/kg DMI for canola meal without and with microbial phytase, respectively, and these values were not different. The TTTD of Ca increased (P < 0.01) if phytase was used but was not affected by the level of dietary Ca. As dietary Ca increased, the amount of Ca absorbed and retained increased (P < 0.01) to a greater extent if phytase was used than when no phytase was included in the diet (interaction, P < 0.05). Fecal P excretion increased (P < 0.01) as dietary Ca increased but was reduced (P < 0.01) by the use of phytase. The ATTD of P decreased (P < 0.01) with increasing dietary Ca to a lesser extent if phytase was used than when no phytase was used (interaction, P < 0.01). In conclusion, endogenous Ca is lost from the gastrointestinal tract of growing pigs, and values for TTTD of Ca are, therefore, different from values for ATTD of Ca. Values for ATTD of Ca are influenced by level of dietary Ca, but that is not the case for values for TTTD of Ca. The ATTD of P decreases as dietary Ca increases, but microbial phytase increases Ca and P digestibility and Ca retention in pigs fed diets based on canola meal whereas it does not influence endogenous losses of Ca.