A climatology atlas of the oxygen situation in the deep water of the Baltic Sea from 1960 to 2011 has been created based on all available data from ICES. Additional data collected during the Baltic International Acoustic Survey (BIAS) have been added to the year 2011. For the autumn period, each profile in the data set was examined for the occurrence of hypoxia (oxygen deficiency) and anoxia (total absence of oxygen). The depths of the onset of hypoxia and anoxia were then interpolated between sampling stations producing two surfaces representing the depth at which hypoxic and anoxic conditions are found. The volume and area of hypoxia and anoxia have been calculated and the results have then been transformed to maps and diagrams to visualize the annual autumn oxygen situation during the analysed period. From the analysed oxygen data 1960-2011 a distinct regime shift has been identified in 1999. During the first regime, 1960 to 1999, hypoxia affected large areas and volumes while anoxic conditions affected only minor deep areas. After the regime shift in 1999 both the areal extent and volume of hypoxia and anoxia are elevated to levels never recorded before. The bottom areas of the Baltic Proper (including the Gulf of Finland and the Gulf of Riga) affected by anoxic conditions have increased from 5%, before the regime shift, to 15% after, i.e. by a factor of 3. The extent of hypoxia has increased from 22% to 28%, i.e. by a factor of~1.3. Excluding the results from 2011, which are preliminary, the largest areal extent of anoxia, 18%, in the Baltic Proper was recorded in 2005 and the largest affected water volume, 10%, was recorded in 2001. The cause and ecosystem effects of the new behaviour of the Baltic Sea that has been recognized after the regime shift, with continuously extreme oxygen conditions, are still not fully understood. However, there are several likely contributory and concurrent causes to the recent development such as changes in winds, changes in frequency and characteristics of inflows, increased loading of organic matter to the deep water, altered vertical mixing and stratification, and changed freshwater runoff. Historically, the oxygen development in the deep water of the Baltic Sea has been investigated in detail and most of the processes involved, both physical and chemical, have been described. But the development during the 2000s is alarming and should be investigated thoroughly. The areal extent and volume of hypoxia have today probably reached the maximal possible extent due to the permanent stratification in the Baltic Proper. However, the extent and volume of anoxic conditions can still increase, which further can enhance the eutrophication of the Baltic Sea due to released phosphorus from sediments that previously have been oxygenated.