Differential scanning calorimetry (DSC) is used to investigate the thermal phase transitions of a range of N-isopropylacrylamide (NIPAM)-based, carboxylic acid-functionalized microgels with well-defined radial and chain functional group distributions. The transition enthalpies of protonated microgels can be correlated with the hydrophobicity of the functional comonomer, while the transition enthalpies for ionized microgels can be correlated with the degree of microgel deswelling achieved across the thermal phase transition. The peak widths at half-height vary inversely with the average length of NIPAM blocks in each of the microgels, as calculated using a kinetic copolymerization model. Deconvolution of the asymmetric DSC thermograms is accomplished using a two-transition model, thought to relate to core-shell-type transitions induced by the significant local heterogeneities within the functionalized microgels. The ratio between the two transition temperatures of these deconvoluted peaks is a useful quantitative probe of the radial functional group distribution. An additional, low-temperature transition is also observed in the thermogram of the vinylacetic acid-functionalized microgel, indicative of the occurrence of local chain rearrangements prior to the macroscopic phase transition in this microgel. Complementary light scattering analysis suggests that microphase separation may account for this additional transition peak.