We studied the low-temperature magnetotransport properties of AlxGa1-xN/AlN/GaN heterostructures with a two-dimensional electron gas (2DEG). Structures with different Al compositions were grown by metal-organic vapor-phase epitaxy on three types of templates: conventional undoped GaN, in situ epitaxial lateral overgrown GaN using a SiNx nanomask layer, and ex situ epitaxial lateral overgrown GaN (ELO-GaN) using a stripe-patterned SiO2 mask. All of the samples display Shubnikov–de Haas (SdH) oscillations that confirm the existence of 2DEGs. Field-dependent magnetoresistance and Hall measurements further indicate that the overgrown heterostructures have a parallel conducting layer in addition to the 2DEG. To characterize the parallel channel, we repeated the measurements after the 2DEG was etched away. 2DEG carrier density values were then extracted from the SdH data, whereas the zero-field 2DEG conductivity was determined by subtracting the parallel channel conductivity from the total. The quantitative mobility spectrum analysis could not be applied in some cases, due to a large contact resistance between the parallel channels. The resulting 2DEG mobility is about a factor of 2 higher in the ELO-GaN and SiN–GaN samples as compared to the standard control samples. The mobility enhancement is attributed to a reduction of threading dislocations by the two ELO techniques employed.