The 32-year-old suffered a hamstring injury in the 3-1 win over Millwall on Saturday and is likely to be out for the next four weeks.
McNaughton had featured in every minute of Bolton’s current seven-match unbeaten run.
The highly-rated defender joined Bolton on loan from Cardiff in September.
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Chelsea have struggled to build momentum in the opening stages of the campaign and are currently looking over their shoulders at the relegation zone.
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