Batten disease (neuronal ceroid lipofuscinoses) comprises a family of autosomal-recessive neurodegenerative diseases characterized by lysosomal accumulation of autofluorescent lipopigment [
1‐
4]. Pathological hallmarks of Batten disease include neuronal death in cortical and thalamic regions of the brain and massive gliosis throughout the CNS, presenting functionally as degeneration of vision, psychomotor delay, and premature death [
5‐
7]. CLN6-Batten disease, resulting from mutations in
CLN6, constitutes two distinct diseases: a pediatric form, also referred to as variant late infantile neuronal ceroid lipofuscinoses, and a rare, less-severe adult-onset form referred to as Kufs type A disease [
8,
9]. The pediatric variant of CLN6 disease begins between the ages of 18 months and 8 years, presenting with language impairment, motor deterioration and cognitive deficiencies, followed by vision loss, seizures, and ultimately premature death during the second decade of life [
10]. There are a number of naturally occurring CLN6 animal models used in therapeutic development, including the
Cln6nclf mouse model that contains a similar point mutation as found in human patients and develops the classical pathophysiological hallmarks of Batten disease, such as intracellular inclusion, retinal degeneration, hind-limb paralysis, and premature death [
11‐
13]. Many of the past Batten disease studies have excluded female mice from therapeutic studies to avoid confounding variables related to sex hormones and chromosomal differences [
14,
15]. However, these biological disease modifiers can potentially limit the translatability of mouse findings to female patients, as sex-based differences that may affect disease susceptibility, disease severity, and therapeutic efficacy [
14]. For example, sex specific symptomatic differences have been reported in other neurodegenerative diseases including Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, and autism spectrum disorders [
14,
16‐
19]. In addition, patient response to therapeutics has varied by sex, as estrogen, testosterone, and other sex-linked genes may affect drug effectiveness [
20].
In the Batten disease field, studies on CLN3-Batten disease, a genetically distinct subtype of Batten disease, have shown differences in disease progression in patients depending on sex [
8,
9,
21,
22]. On average, female CLN3-Batten disease patients present with symptoms 1 year later than their male counterparts, have accelerated disease progression following symptom onset, and die 1 year earlier than males [
21]. Initial characterization of the
Cln3Δ7/8 murine model did not consider sex-based differences, however, recent work with this model has demonstrated that females exhibit poorer performance in behavioral tests [
23,
24]. Additionally, the naturally occurring mouse model of CLN8-Batten disease has shown sex differences in female
Cln8mnd mice, where female retinas exhibited higher levels of retinal oxidative stress and caspase-3 activity compared to males [
25]. These findings prompted us to investigate sex discrepancies in outcomes associated with CLN6 disease, exploring differences in disease onset and progression between male and female
Cln6nclf mice. We describe subtle histopathological differences between the sexes and a more rapid disease progression in female
Cln6nclf mice. Consequently, including sex as a factor during studies and subsequent analyses can ensure proper development of therapeutic treatments for patients with CLN6 disease.