According to the documentation the DEFAULT_KERNEL_CONFIG option should set the default kernel config overriding /usr/share/genkernel/arch/<arch>/generated-config however after deleting my saved config in /etc/kernels/ and setting the default to /etc/kernels/base-config.conf genkernel was still using the generated-config file. To be sure the generated-config wasn't based off of my supplied config I diffed them and they are extremely different kernel configs. forcing the config with --kernel-config does still work. sys-kernel/genkernel-4.2.6-r8 (stable) # from my /etc/genkernel.conf DEFAULT_KERNEL_CONFIG="/etc/kernels/base-config.conf"