Several studies have pointed out that the Autonomous Regions of Navarre and Basque Country show higher brain cancer incidence [
1] and mortality [
2,
3] risks than the rest of the Spanish regions. According to the latest estimated data published by the GLOBOCAN project, in 2012 a total of 2,056 and 1,661 new brain cancer cases were diagnosed in Spanish male and female population respectively, representing 6.1 and 4.2 cases per 100,000 inhabitants (age-standardized rates adjusted to world population) [
4]. Although these rates are below the European average (6.3 and 4.6 in males and females respectively), data from the International Agency for Research on Cancer (IARC) showed that during the period 2003–2007, brain cancer incidence rates in Navarre and Basque Country provinces were among the highest rates registered for all regions and both genders [
5]. With the aim of determining the possible causes that explain these high risk clusters in Spain, an exhaustive geographical study of the potential influence of land use variables was assessed [
6]. No evidence on the possible association between the specific type of crop or land use and the distribution of the disease was found. Recently, a study of brain and central nervous system (CNS) cancer incidence in Navarre was performed to describe temporal trends of cancer incidence rates during the period 1973–2008 [
7]. In that work, the area was considered as an explanatory variable dividing the observed cases into urban and non-urban areas. However, the geographical distribution of the disease within Navarre was not analyzed. A study of spatial mortality patterns for several cancer locations (stomach, colorectal, lung, breast, prostate and urinary bladder cancer) was also recently performed on 8,073 Spanish municipalities during the period 1989–2008 [
8], but brain cancer was not studied. In this paper our interest lies in analyzing the temporal evolution of the geographical distribution of brain cancer incidence in the municipalities of Navarre and Basque Country. We are mainly interested in locating high risk municipalities within both Autonomous Regions. Health areas constituted by several municipalities were also considered as a new level of spatial aggregation to gain power in our analysis. According to the literature, just a small percentage of brain cancer cases can be explained by the only clearly established risk factors: genetic and environmental factors [
9,
10], and ionizing radiations [
11,
12]. This lack of clearly established factors is the reason why the analysis performed here becomes so crucial.