Voltage-gated K⁺ (Kv) channels related to the Shal gene of Drosophila (Kv4 channels) carry a somatodendritic A-type current, which mediates synaptic filtering and controls the generation and backpropagation of action potentials. Kv4 channel complexes may contain cytoplasmic accessory b-subunits, the Kv Channel Interacting Proteins (KChIPs). KChIPs increase the amount of surface expression and modulate the inactivation gating of Kv4 channels. Four different KChIP genes encode similar but distinct KChIP subtypes (KChIP1, KChIP2, KChIP3 and KChIP4). KChIP3 is special, since it does not only interact with Kv4 channels but also with the Ca²⁺ signaling protein presenilin (KChIP3 = calsenilin), and, when located in the nucleus, may bind to DNA and act as a transcription repressor (KChIP3 = downstream regulatory element antagonist modulator; DREAM). More recently, it was reported that KChIP3 also interacts with the lysosomal membrane protein CLN3 (ceroid-lipofuscinosis, neuronal 3). Gene defects in CLN3 are associated with Juvenile Neuronal Ceroid Lipofuscinosis (JNCL), also known as CLN3 disease juvenile phenotype or Batten disease. The present study was undertaken to find out whether and how CLN3, by its putative interaction with KChIP3, may modulate Kv4.2/KChIP3 channel function, and whether mutations in CLN3 play a role in this form of modulation. To this end, we coexpressed the putative interaction partners KChIP3 and CLN3 either individually or both together with Kv4.2 by transient cDNA transfection in Human Embryonic Kidney (HEK) 293 cells. We performed coimmunoprecipitation experiments to examine the effect of CLN3 on the Kv4.2/KChIP3 interaction and whole-cell patch-clamp recordings to analyse Kv4.2-mediated macroscopic currents. Our coimmunoprecipitation data indicate a lower amount of KChIP3 bound to Kv4.2 in the presence of CLN3. Coexpression of Kv4.2 with KChIP3 caused a typical increase in current density, slowing of macroscopic inactivation, acceleration of recovery from inactivation and a positive shift in the voltage dependence of steady-state inactivation. KChIP3 also caused a negative shift in the Kv4.2 activation curve. Coexpression of CLN3 with Kv4.2 and KChIP3 suppressed the observed KChIP effects, with stronger suppression on the second than on the first day after transfection. Notably, the suppression of KChIP effects was weaker for the JNCL-related point mutant CLN3 R334C and almost absent for a JNCL-related deletion mutant (CLN3 del). Our data support the notion that the control of somatodendritic A-type channel function involves CLN3. The CLN3-mediated control may be impaired or completely lost in JNCL.